Molecular Genetics and Breeding of Forest Trees.

bout the Editors xiii Contributors xv Preface xix PART I: FOREST TREE FUNCTIONAL GENOMICS Chapter 1. Functional Genomics in Forest Trees 3 Alison M. Morse Janice E. K. Cooke John M. Davis Introduction 3 The Functional Genomics Tool Kit—Transcript Discovery and Profiling 4 Functional Genomics in Action 10 En Route to Functional Genomics in Forest Trees 12 Conclusions 15 Chapter 2. Expressed Sequence Tag Databases from Forestry Tree Species 19 Timothy J. Strabala Introduction 19 Forestry Tree EST Databases 21 The Genesis Pine and Eucalyptus EST Projects 26 Special Purpose Libraries 41 Conclusion 47 Chapter 3. Proteomics for Genetic and Physiological Studies in Forest Trees: Application in Maritime Pine 53 Christophe Plomion Jean-Marc Gion Nasser Bahrman Céline Lalanne Paulo Costa Delphine Madur Christian Dubos Cédric Pionneau Jean-Marc Frigerio Sophie Gerber Introduction 53 Characterization of the Pine Proteome 55 Genetic Variability of Qualitative and Quantitative Protein Variants 62 Variability of Proteome Expression in Physiological Studies 68 Conclusion 73 Chapter 4. Exploring the Transcriptome of the Ectomycorrhizal Symbiosis 81 Francis Martin Annegret Kohler Sébastien Duplessis Denis Tagu Introduction 81 The Ectomycorrhizal Symbiosis 82 The Anatomy and Development of Ectomycorrhiza 83 The Morphogenesis of Ectomycorrhiza 86 Alteration in Gene Expression in Ectomycorrhiza 87 The Transcriptome of Ectomycorrhizal Symbioses 90 Outlook 102 PART II: MOLECULAR BIOLOGY OF WOOD FORMATION Chapter 5. Genomics of Wood Formation 113 Jae-Heung Ko Sunchung Park Jaemo Yang Kyung-Hwan Han Sookyung Oh Introduction 113 Wood Biosynthesis 114 Regulation of Wood Formation 120 Arabidopsis As a Model for the Study of Wood Formation 123 Genomics Approach to Wood Formation 124 The Outlook 132 Chapter 6. Molecular Genetics of Cellulose Biosynthesis in Trees 141 Chandrashekhar P. Joshi Introduction 141 Cellulose Heterogeneity in Trees 142 Cellulose Production Under Mechanical Stress 143 The Site of Cellulose Biosynthesis 144 Current Knowledge of the General Process of Cellulose Synthesis in Plants 145 Identification of CesA Genes in Plants 146 Isolation of New CesA and CSLD Genes 151 Future Perspectives 162 Chapter 7. Tuning Lignin Metabolism Through Genetic Engineering in Trees 167 Lise Jouanin Thomas Goujon Introduction 167 Genetic Modification of PAL and C4H 171 Genetic Modification of 4CL 174 Genetic Modification of C3H 174 Genetic Modification of CCoAOMT 175 Genetic Modification of CCR 175 Genetic Modification of F5H 176 Genetic Modification of COMT 177 Genetic Modification of CAD 179 Genetic Modification of Peroxidases and Laccases 181 Genetic Modification of Transcription Factors 182 Outlook 183 Chapter 8. In Vitro Systems for the Study of Wood Formation 193 Mathew A. Leitch Gerd Bossinger Introduction 193 Cambial Activity 194 Wood Formation 194 The Formation of Tracheary Elements 195 Heartwood Formation (Tylosis and Pit Aspiration) 196 In Vitro Wood Formation Systems 199 Future Perspectives 203 PART III: FOREST TREE TRANSGENESIS Chapter 9. Genetic Modification in Conifer Forestry: State of the Art and Future Potential—A Case Study with Pinus radiata 215 Christian Walter Armando McDonald Julia Charity Ralf Möller Lloyd Donaldson Armin Wagner Lynette Grace Introduction 215 Tissue Culture As a Tool for Molecular Research 216 Genetic Engineering in Conifers 218 Modification of Traits by Suppression of Gene Expression 222 Analysis of Promoters Controlling Gene Expression in Conifers 224 Tissue Culture Protocols for the Early Assessment of Gene Function 226 Tools to Assess Gene Function at the Micro Level 230 Conclusions 235 Chapter 10. Transgenic Forest Trees for Insect Resistance 243 Wang Lida Han Yifan Hu Jianjun Introduction 243 Woody Plant Species Transgenic to Insect-Resistant Genes 244 Insect-Resistant Genes 248 Field Performance of Insect-Resistant Transgenic Trees 251 Biosafety of Insect-Resistant Transgenic Plants 254 Conclusion and Outlook 255 Chapter 11. Modification of Flowering in Forest Trees 263 Juha Lemmetyinen Tuomas Sopanen Introduction 263 Regulation of Flowering Time and Flower Development in Arabidopsis 264 Genes Regulating Flower Development in Trees 267 Prevention of Flowering 275 Acceleration of Flowering 281 Conclusions 283 Chapter 12. Stability of Transgene Expression in Aspen 293 Sandeep Kumar Matthias Fladung Introduction 293 rolC Gene, a Phenotypic Marker for the Stability of Transgene Expression 294 Morphological Analysis of 35S-rolC Transgenic Aspen Plants 295 Transgene Silencing 297 Transgene Repeat Formation and Unstable Expression 297 Transgene Integration and Unstable Expression 300 Mechanisms of Transgene Integration and Repeat Formation 300 How to Obtain Stably Expressing Transgenic Plants 302 Future Perspectives 303 Chapter 13. Asexual Production of Marker-Free Transgenic Aspen Using MAT Vector Systems 309 Hiroyasu Ebinuma Saori Endo Koichi Sugita Keiko Yamada-Watanabe Etsuko Matsunaga Introduction 309 Transformation Methods Using Agrobacterium 310 Problems of Antibiotic Selection 311 Principles of the MAT (Multi-Auto-Transformation) Vector System 313 Two-Step Transformation of Tobacco Plants Using the GST-MAT Vector 316 Transformation of Hybrid Aspen Using the GST-MAT Vector 320 Current Techniques for Removing Selectable Markers and Their Problems 323 Advantages of Selection Using the ipt Gene 327 Transgene Stacking Using the ipt-MAT Vector 329 Combination of the ipt and iaaM/H Genes 331 Decrease in Environmental Impact Using Sterile Transgenic Trees 334 Conclusion 335 PART IV: GENOME MAPPING IN FOREST TREES Chapter 14. High-Density Linkage Maps in Conifer Species and Their Potential Application 341 Enrique Ritter Jean-Michel Favre Santiago Espinel Matthias Fladung Introduction 341 Basic Aspects for Constructing High-Density Maps in Conifer Species 342 Application of High-Density Maps in Forest Species 347 Conclusions and Perspectives 352 Chapter 15. Microsatellites in Forest Tree Species: Characteristics, Identification, and Applications 359 Giovanni G. Vendramin Ivan Scotti Birgit Ziegenhagen Introduction 359 Microsatellites in the Nuclear Genome: Distribution and Variability 360 From Genome to Populations: The Isolation of Microsatellites and the Development of Molecular Markers 364 Microsatellites in Populations: SSRs As a Tool for the Screening of Diversity, Differentiation, and Evolution 365 What is Different About Microsatellites of the Organelle Genomes? 370 Conclusions 378 Chapter 16. Genome Mapping in Populus 387 María Teresa Cervera Véronique Storme Mitchell M. Sewell Wout Boerjan Patricia Faivre-Rampant Introduction 387 Marker Systems 388 Mapping Strategies 389 Genetic Linkage Maps of the Populus Genome 389 Comparison of Linkage Maps 404 Perspectives 406 Chapter 17. Genetic Mapping in Acacias 411 Penelope A. Butcher Introduction 411 Aspects of the Reproductive Biology of Acacias That Affect Genetic Mapping Strategies 412 Linkage Mapping in Acacia mangium 414 Applications of the Acacia Map 420 Conclusions 422 Index 429